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DEseq
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0
votes
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40
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 12 hours ago by
ATpoint
★ 2.0k • written 1 day ago by
m-bihie
• 0
0
votes
1
reply
104
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 9 days ago by
Dario Strbenac
★ 1.5k • written 11 days ago by
Hicham
• 0
0
votes
2
replies
759
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 11.0 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
173
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 4 months ago by
ATpoint
★ 2.0k • written 4 months ago by
barrypraveen
• 0
3
votes
2
replies
285
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
6 months ago
manwar
• 0
1
vote
1
reply
278
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 7 months ago by
Michael Love
39k • written 7 months ago by
stew
• 0
1
vote
5
replies
404
views
Error in DEseq
DEseq
RNASeqData
updated 7 months ago by
ATpoint
★ 2.0k • written 7 months ago by
Sanatan
• 0
2
votes
1
reply
442
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
1
vote
5
replies
583
views
Potential outlier/high variance
deseq
DESeq2
updated 9 months ago by
Michael Love
39k • written 9 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
330
views
Deseq2 with imbalanced design
Deseq
10 months ago
Alex
• 0
1
vote
4
replies
657
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 12 months ago by
Michael Love
39k • written 12 months ago by
penny.lane
• 0
0
votes
2
replies
478
views
DESeqDataSet design issue
DESeq
DESeq2
13 months ago
matthew.valentine
• 0
1
vote
1
reply
590
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 15 months ago by
Michael Love
39k • written 15 months ago by
n.vandis
• 0
4
votes
6
replies
858
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
16 months ago
s-rhussien
• 0
2
votes
2
replies
1.1k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
17 months ago • updated 16 months ago
jbnrodriguez
▴ 10
1
vote
2
replies
448
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
17 months ago
krawczyk.margarita
• 0
0
votes
2
replies
668
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 17 months ago by
Michael Love
39k • written 17 months ago by
aiswaryabioinfo
• 0
0
votes
1
reply
480
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
20 months ago
ayy2110
• 0
1
vote
2
replies
533
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 22 months ago by
ericfournier2
▴ 10 • written 23 months ago by
GM
▴ 10
0
votes
3
replies
1.1k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 23 months ago by
Michael Love
39k • written 23 months ago by
sp
• 0
0
votes
5
replies
949
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 24 months ago by
Michael Love
39k • written 24 months ago by
rowcyclecamp
• 0
2
votes
12
replies
3.2k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 2.2 years ago by
Michael Love
39k • written 7.7 years ago by
Nick
• 0
1
vote
2
replies
572
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
2.6 years ago
canfield
▴ 10
0
votes
7
replies
730
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 2.7 years ago by
Kevin Blighe
3.7k • written 2.7 years ago by
maniermk
• 0
2
votes
4
replies
2.4k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
updated 11 months ago by
Nicola
• 0 • written 2.8 years ago by
krunal.24.6
▴ 10
1
vote
2
replies
375
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 2.8 years ago by
Simon Anders
★ 3.7k • written 2.8 years ago by
blawney
• 0
3
votes
5
replies
1.0k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 2.8 years ago by
Michael Love
39k • written 2.8 years ago by
svlachavas
▴ 800
1
vote
9
replies
659
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 2.9 years ago by
Simon Anders
★ 3.7k • written 2.9 years ago by
megapode32559
• 0
0
votes
7
replies
583
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
3.0 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
679
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 3.1 years ago by
Michael Love
39k • written 3.1 years ago by
mrfossl97
▴ 10
2
votes
3
replies
807
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 3.2 years ago by
Michael Love
39k • written 3.2 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
2.3k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 3.5 years ago by
wunderl
▴ 30 • written 3.5 years ago by
neekonsu
• 0
1
vote
2
replies
515
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 3.5 years ago by
Michael Love
39k • written 3.5 years ago by
sxv
• 0
0
votes
0
replies
596
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
3.6 years ago
kentfung
▴ 10
0
votes
9
replies
1.1k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
3.9 years ago
ariel
▴ 10
3
votes
12
replies
912
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
3.9 years ago
ariel
▴ 10
2
votes
3
replies
1.2k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 4.1 years ago by
Michael Love
39k • written 4.1 years ago by
lefeverde
▴ 10
0
votes
1
reply
595
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 4.2 years ago by
Michael Love
39k • written 4.2 years ago by
FaisalH
• 0
0
votes
3
replies
729
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
4.3 years ago
Ben
▴ 50
0
votes
7
replies
3.2k
views
DESeq2 install problem
deseq
updated 4.3 years ago by
Michael Love
39k • written 4.3 years ago by
bikashten
• 0
4
votes
7
replies
2.4k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 4.3 years ago by
Michael Love
39k • written 4.3 years ago by
thindmarsmission
• 0
0
votes
3
replies
658
views
DESeq2 group comparison
deseq2
deseq
differential binding analysis
updated 4.3 years ago by
Michael Love
39k • written 4.3 years ago by
rbronste
▴ 60
3
votes
5
replies
725
views
Help with multi-factor Deseq analysis
deseq2
rnaseq
deseq
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
MAPK
• 0
0
votes
7
replies
774
views
Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
Matthew.baldwin
• 0
4
votes
1
reply
13k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
4.4 years ago
ansari.sarabio
• 0
1
vote
5
replies
696
views
Group Specific Condition Query
deseq2
deseq
batcheffect
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
bdy8
• 0
3
votes
7
replies
710
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2
deseq
4.5 years ago
blastzone.heimerdinger
▴ 10
0
votes
8
replies
1.4k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq
deseq2
deseq
R
updated 4.5 years ago by
Michael Love
39k • written 4.5 years ago by
arun.thirumaran
• 0
0
votes
1
reply
510
views
how to start normalization
deseq
4.5 years ago
raghavaraghava049
• 0
0
votes
1
reply
611
views
Basemean always multiples of 0.5 in deseq2 results
deseq
results
baseMean
updated 4.5 years ago by
Michael Love
39k • written 4.5 years ago by
batmaiden
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot
by
Nathalie
• 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Comment: Design for DE analysis in tidybulk
by
Michael Love
39k
The mapping from what you want to a contrast is a long conversation. You can make pairwise comparisons or numeric contrasts or really anyth…
Comment: MA plot
by
Guido Hooiveld
★ 3.5k
Without having a reproducible example, or access to your data, it is almost impossible to help you. Also note that `ggpubr` is not a Biocon…
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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